FAIRMol

Z44856623

Pose ID 9308 Compound 3184 Pose 500

DB SELECTIONDocking pose analysis is being read from this database.
Compound detail Protein structures Back to compounds
Molecular metrics status: done
RDKit SASA-based burial metrics are cached.
SASA cached
T14
T. brucei ODC (G418 binding site) T. brucei G418 binding site
Ligand Z44856623
PDB1NJJ↗

3D complex viewer

Strict H-bonds Permissive H-bonds
Viewer legend
Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Reject SASA cached
Likely artefact or unreliable pose
Binding strong Geometry medium Native mixed SASA done
Strain ΔE
29.9 kcal/mol
Protein clashes
3
Internal clashes
3
Native overlap
contact recall 0.53, Jaccard 0.33, H-bond role recall 0.20
Burial
75%
Hydrophobic fit
76%
Reason: no major geometry red flags detected
3 protein-contact clashes 3 intramolecular clashes
Molecular report
Full metrics ↗
Reject Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-0.503 kcal/mol/HA) ✓ Good fit quality (FQ -5.00) ✓ Good H-bonds (5 bonds) ✓ Deep burial (75% SASA buried) ✓ Lipophilic contacts well-matched (76%) ✗ High strain energy (29.9 kcal/mol) ✗ Geometry warnings ✗ Protein-contact clashes (6) ✗ Many internal clashes (11)
Score
-16.615
kcal/mol
LE
-0.503
kcal/mol/HA
Fit Quality
-5.00
FQ (Leeson)
HAC
33
heavy atoms
MW
500
Da
LogP
4.46
cLogP
Strain ΔE
29.9 kcal/mol
SASA buried
75%
Lipo contact
76% BSA apolar/total
SASA unbound
744 Ų
Apolar buried
424 Ų

Interaction summary

HB 5 HY 13 PI 0 CLASH 3
Final rank1.559Score-16.615
Inter norm-0.710Intra norm0.196
Top1000noExcludedno
Contacts17H-bonds5
Artifact reasongeometry warning; 11 clashes; 6 protein contact clashes; moderate strain Δ 29.9
Residues
ARG22 ARG342 ARG50 ASN20 ASP44 CYS26 GLN341 GLU343 GLU384 ILE345 LEU25 LEU382 PRO340 PRO344 SER410 THR21 THR285

Protein summary

398 residues
Protein targetT14Atoms6140
Residues398Chains1
Residue summaryVAL:592; LEU:513; LYS:484; ARG:432; PHE:420; ILE:418; ASP:349; THR:322; TYR:315; PRO:308; GLU:301; ALA:290; SER:253; GLY:217; ASN:210; GLN:170

Receptor context

1 kept / 0 excluded
Receptor context filtering: interactions and SASA are computed against protein atoms plus allowed cofactors/ions. Native ligand-like HETATM partners are excluded from scoring.
Kept context 1 Excluded HETATM 0
Kept cofactors / ions
A:ORX602

Native ligand reference

★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
Name1NJJContacts15
PoseOpen native poseHB0
IFP residues
ARG22 ARG242 ARG337 ARG342 ASP243 ASP385 GLN341 GLU384 LEU25 LEU339 LEU382 PRO340 PRO344 SER282 THR241
Current overlap8Native recall0.53
Jaccard0.33RMSD-
HB strict1Strict recall0.17
HB same residue+role1HB role recall0.20
HB same residue1HB residue recall0.20

HB · H-bonds
Mode: strict. Count shows atom-level H-bonds; unique residues in summary: 0.

PI · π–π interactions
No pi · π–π interactions detected for this pose.

HY · Hydrophobic contacts

CLASH · Clashes

All stored poses for this docking hit

PoseFinal rankInter normScoreHBCTCT overlapCT recallHB role rec.RMSDExcluded
495 0.950159587799313 -0.862578 -27.4867 2 17 0 0.00 0.00 - no Open
500 1.558892349383295 -0.709759 -16.6151 5 17 8 0.53 0.20 - no Current
500 5.094929360837185 -0.918857 -23.6809 11 20 0 0.00 0.00 - no Open

Molecular metrics

RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
✓ Metrics available

Scoring & efficiency
Docking score -16.615kcal/mol
Ligand efficiency (LE) -0.5035kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -4.996
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 33HA

Physicochemical properties
Molecular weight 500.0Da
Lipinski: ≤ 500 Da
LogP (cLogP) 4.46
Lipinski: ≤ 5
Rotatable bonds 7

Conformational strain (MMFF94s)
Strain energy (ΔE) 29.93kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 87.76kcal/mol
Minimised FF energy 57.83kcal/mol

SASA & burial

✓ computed
SASA (unbound) 744.2Ų
Total solvent-accessible surface area of free ligand
BSA total 555.1Ų
Buried surface area upon binding
BSA apolar 424.4Ų
Hydrophobic contacts buried
BSA polar 130.7Ų
Polar contacts buried
Fraction buried 74.6%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 76.5%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -2531.0Ų
SASA_nonpolar(complex) − SASA_nonpolar(receptor) − SASA_nonpolar(ligand free). Negative = non-polar surface buried upon binding. Requires full polarity-decomposed SASA computation.
Receptor non-polar SASA 3349.0Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 1395.4Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)